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<!DOCTYPE html>
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<title>Relion Cryoem for Satorians — MIT Satori User Documentation documentation</title>
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<li class="toctree-l2"><a class="reference internal" href="#quick-start">Quick start</a></li>
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<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-linux-kernel-level-am-i-running">What Linux kernel level am I running?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-software-levels-are-installed-on-the-system">What software levels are installed on the system?</a></li>
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<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#system-hardware-queries">System hardware queries</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-is-my-cpu-configuration">What is my CPU configuration?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-much-ram-is-there-on-my-nodes">How much RAM is there on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-smt-mode-are-my-nodes-in">What SMT mode are my nodes in?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-cpu-governor-is-in-effect-on-my-nodes">What CPU governor is in effect on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-are-the-logical-ids-and-uuids-for-the-gpus-on-my-nodes">What are the logical IDs and UUIDs for the GPUs on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-is-the-ibm-model-of-my-system">What is the IBM model of my system?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#which-logical-cpus-belong-to-which-socket">Which logical CPUs belong to which socket?</a></li>
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<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-set-a-time-limit-on-my-job">How do I set a time limit on my job?</a></li>
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<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-deselect-specific-nodes-for-my-job">How do I deselect specific nodes for my job?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#my-jobs-runtime-environment-is-different-from-what-i-expected">My job’s runtime environment is different from what I expected</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#i-want-to-know-precisely-what-my-jobs-runtime-environment-is">I want to know precisely what my job’s runtime environment is</a></li>
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<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html">How do I build a Singularity image from scratch?</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#run-docker-in-ppc64le-mode-on-an-x86-machine-to-generate-an-image-for-satori">Run Docker in ppc64le mode on an x86 machine to generate an image for Satori</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#import-new-docker-hub-image-into-singularity-on-satori">Import new Docker hub image into Singularity on Satori</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#using-singularity-instead-of-docker">Using Singularity instead of Docker</a></li>
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<li>Relion Cryoem for Satorians</li>
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<div class="section" id="relion-cryoem-for-satorians">
<h1>Relion Cryoem for Satorians<a class="headerlink" href="#relion-cryoem-for-satorians" title="Permalink to this headline">¶</a></h1>
<div class="section" id="prerequisites">
<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline">¶</a></h2>
<p>A local installation of an X11 server is required to use the Relion GUI.</p>
<p>On a Mac computer the XQuartz ( <a class="reference external" href="https://www.xquartz.org" target="_blank">https://www.xquartz.org</a> ) software is a good option.</p>
<p>On a Window computer Cygwin/X ( <a class="reference external" href="http://x.cygwin.com" target="_blank">http://x.cygwin.com</a> ) software provides a free X server.</p>
</div>
<div class="section" id="quick-start">
<h2>Quick start<a class="headerlink" href="#quick-start" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Transfer data</li>
</ul>
<p>Data should be transferred to:
/nobackup/users/<code class="docutils literal notranslate"><span class="pre">your_kerbos_id</span></code> .
Use satori-login-002.mit.edu</p>
<ul>
<li><p class="first">To access the Relion GUI</p>
<ol class="arabic">
<li><p class="first">Login:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ssh -Y [email protected]
</pre></div>
</div>
</li>
<li><p class="first">Submit a fake job to access a node:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>bsub -q normal sleep <span class="m">7200</span>
</pre></div>
</div>
</li>
<li><p class="first">Use bjobs to determine the node of the job ie:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
<span class="m">45954</span> seyvos RUN normal service0002 node0028.in sleep <span class="m">7200</span> Mar <span class="m">10</span> <span class="m">13</span>:50
</pre></div>
</div>
</li>
<li><p class="first">Login into the node:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ssh -X node0028
</pre></div>
</div>
</li>
<li><p class="first">Add paths to access relion libraries:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span>/nobackup/users/ruzhu/RELION/bin:/nobackup/users/ruzhu/CTFfind4/bin:/opt/ibm/spectrum_mpi/bin:<span class="nv">$PATH</span>
<span class="nb">export</span> <span class="nv">LD_LIBRARY_PATH</span><span class="o">=</span>/opt/ibm/spectrum_mpi/profilesupport/lib:/nobackup/users/ruzhu/CTFfind4/lib:<span class="nv">$LD_LIBRARY_PATH</span>
</pre></div>
</div>
</li>
<li><p class="first">Open Relion by typing:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>relion
</pre></div>
</div>
</li>
<li><p class="first">Use GUI to configure your job.</p>
</li>
<li><p class="first">Use “Print” command to print job commands to terminal.</p>
</li>
<li><p class="first">Adjust the relion submission script to incorporate the commands specific to your job. Note: If you have a job that requires a lot of memory, you should alter the <code class="docutils literal notranslate"><span class="pre">--n</span></code> and <code class="docutils literal notranslate"><span class="pre">--j</span></code> values. Save submission script. Make sure paths for <code class="docutils literal notranslate"><span class="pre">--o</span></code> already exist.</p>
</li>
<li><p class="first">Execute job</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>bsub< run
</pre></div>
</div>
</li>
<li><p class="first">Check job is running with bjobs. Submission script generates a log file.</p>
</li>
</ol>
</li>
<li><p class="first">Example job</p>
</li>
</ul>
<p>Below is an example of a job file that Relion should generate. The file you generate should look something
like this.</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1">#BSUB -L /bin/bash</span>
<span class="c1">#BSUB -J "Relion"</span>
<span class="c1">#BSUB -o "Relion.%J"</span>
<span class="c1">#BSUB -n 40</span>
<span class="c1">#BSUB -R "span[ptile=40]"</span>
<span class="c1">#BSUB -gpu "num=4"</span>
<span class="c1">#BSUB -q "normal"</span>
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span>/nobackup/users/ruzhu/RELION/bin:/nobackup/users/ruzhu/CTFfind4/bin:/opt/ibm/spectrum_mpi/bin:<span class="nv">$PATH</span>
<span class="nb">export</span> <span class="nv">LD_LIBRARY_PATH</span><span class="o">=</span>/nobackup/users/ruzhu/CTFfind4/lib:<span class="nv">$LD_LIBRARY_PATH</span>
<span class="c1">#source ~/anaconda3/bin/activate</span>
<span class="c1">#conda activate CryoEM</span>
<span class="nb">unset</span> CUDA_VISIBLE_DEVICES
<span class="nb">export</span> <span class="nv">CUDA_VISIBLE_DEVICES</span><span class="o">=</span><span class="s2">"0,1,2,3"</span>
<span class="o">(</span><span class="nb">time</span> -p mpirun -bind-to none -n <span class="m">9</span> relion_refine_mpi --j <span class="m">4</span> --gpu --pool <span class="m">50</span> --dont_combine_weights_via_disc --scratch_dir /dev/shm --o Refine3D/job005 --auto_refine --split_random_halves --i squirrel2.star --ref Import/job004/postprocess_refine850_resampled_775.mrc --firstiter_cc --ini_high <span class="m">40</span> --ctf --ctf_corrected_ref --particle_diameter <span class="m">340</span> --flatten_solvent --zero_mask --oversampling <span class="m">1</span> --healpix_order <span class="m">2</span> --auto_local_healpix_order <span class="m">4</span> --offset_range <span class="m">5</span> --offset_step <span class="m">2</span> --sym C1 --low_resol_join_halves <span class="m">40</span> --norm --scale<span class="o">)</span> >run_21x8.log <span class="m">2</span>><span class="p">&</span><span class="m">1</span>
</pre></div>
</div>
</div></blockquote>
</div>
<div class="section" id="other-notes">
<h2>Other notes<a class="headerlink" href="#other-notes" title="Permalink to this headline">¶</a></h2>
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